Preparations for Europe's first major film festival of the year were overshadowed by a newspaper report last month alleging Bauer had been more involved in the Nazi regime than previously thought.
The "Alfred Bauer prize" has been removed from Saturday's awards ceremony, and the Berlinale has commissioned the Munich-based Institute for Contemporary History (IfZ) to investigate its founding director's Nazi ties.
"With Alfred Bauer, it is probably the case that certain voices raised (his Nazi links) at the time, but it was swept under the carpet and is only coming out again now," IfZ director Andreas Wirsching told AFP.
Whitewashing
While the festival wrestles with its own history, a number of films on the programme set out to challenge dominant narratives about the past.
In "Speer Goes To Hollywood", which premiered in Berlin this week, Israeli director Vanessa Lapa documents the efforts of Nazi architect Albert Speer to whitewash his image after the war.
The highest ranking Nazi not to be sentenced to death at the Nuremberg trials, Speer's memoirs later became a best-selling book and never-made Hollywood film project.
Using conversations between Speer and producer Andrew Birkin, Lapa subtly exposes the absurdity of the architect's reputation as the "Good Nazi".
"Speer is a good example of how long an accepted Nazi perpetrator could tell his own story as if he and those in his milieu didn't have so much to do with it," IfZ director Wirsching told AFP.
Whitewashing the past is also an issue in Brazil, according to director Marco Dutra, whose film "All the Dead Ones" is up for the Golden Bear in Berlin.
Brazil's far-right president Jair Bolsonaro has claimed racism is "rare" in the country and recently appointed Sergio Camargo as head of the institute for Afro-Brazilian culture -- a man who has said slavery was "beneficial" to those of African descent.
Dutra takes the opposite view with "All the Dead Ones", which is set in late 19th century Sao Paulo, a decade on from the abolition of slavery.
"Despite numerous, still respected theories which claim that Brazil is built on a mix of identities, the reality is very different. It is a very racist country," he said.
Hiroshima and the Holocaust
Another Golden Bear candidate, Rithy Panh, added that cinema had a role to play in the "fight against totalitarianism".
Panh's film "Irradiated" confronts the viewer with harrowing images of both Hiroshima and the Holocaust.
"The film is a cry of hope, a cry to conjure misery. We think that these things are in the last century, but they are repeating themselves again and again," said the French-Cambodian director.
Nigerian director and archivist Didi Cheeka of the Lagos Film Society, meanwhile, believes that cinema can help a society come to terms with its past.
"It is always much more dangerous when images are suppressed," said Cheeka, whose short film "Memory Also Die" uses previously forgotten footage from post-war Nigeria.
Speaking to AFP at the Berlinale, he said archive film could challenge "official narratives" about the brutal Biafra War, which nearly tore apart newly independent Nigeria in the late 1960s.
Cheeka argued that because people were encouraged not to talk about the conflict for decades, resentments are now bubbling up in modern Nigeria.
"I see resentment in my part of the country, which lost the war... people are now talking about it in a bitter, resentful way."
By restoring footage of the war from the colonial-era archives, Cheeka aims to "help bridge this divide and help people come to terms with what happened."
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